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Synthetic genome with recoding

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References

  • Blount, B.A., Gowers, G.O.F., Ho, J.C.H., Ledesma-Amaro, R., Jovicevic, D., McKiernan, R.M., Xie, Z.X., Li, B.Z., Yuan, Y.J., and Ellis, T. (2018). Rapid host strain improvement by in vivo rearrangement of a synthetic yeast chromosome. Nat Commun 9, 1932.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dymond, J.S., Richardson, S.M., Coombes, C.E., Babatz, T., Muller, H., Annaluru, N., Blake, W.J., Schwerzmann, J.W., Dai, J., Lindstrom, D. L., et al. (2011). Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature 477, 471–476.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Deng, G., Lu, Y., Zlotnikov, G., Thor, A.D., and Smith, H.S. (1996). Loss of heterozygosity in normal tissue adjacent to breast carcinomas. Science 274, 2057–2059.

    Article  CAS  PubMed  Google Scholar 

  • Fredens, J., Wang, K., de la Torre, D., Funke, L.F.H., Robertson, W.E., Christova, Y., Chia, T., Schmied, W.H., Dunkelmann, D.L., Beránek, V., et al. (2019). Total synthesis of Escherichia coli with a recoded genome. Nature 569, 514–518.

    Article  CAS  PubMed  Google Scholar 

  • Hochrein, L., Mitchell, L.A., Schulz, K., Messerschmidt, K., and Mueller-Roeber, B. (2018). L-SCRaMbLE as a tool for light-controlled Cremediated recombination in yeast. Nat Commun 9, 1931.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Isaacs, F.J., Carr, RA., Wang, H.H., Lajoie, M.J., Sterling, B., Kraal, L., Tolonen, A.C., Gianoulis, T.A., Goodman, D.B., Reppas, N.B., et al. (2011). Rrecise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science 333, 348–353.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jia, B., Wu, Y., Li, B.Z., Mitchell, L.A., Liu, H., Ran, S., Wang, J., Zhang, H.R., Jia, N., Li, B., et al. (2018). Precise control of SCRaMbLE in synthetic haploid and diploid yeast. Nat Commun 9, 1933.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Koufos, A., Hansen, M.F., Copeland, N.G., Jenkins, N.A., Lampkin, B.C., and Cavenee, W.K. (1985). Loss of heterozygosity in three embryonal tumours suggests a common pathogenetic mechanism. Nature 316, 330–334.

    Article  CAS  PubMed  Google Scholar 

  • Li, Y., Wu, Y., Ma, L., Guo, Z., Xiao, W., and Yuan, Y. (2019). Loss of heterozygosity by SCRaMbLEing. Sci China Life Sci 62, 381–393.

    Article  PubMed  Google Scholar 

  • Liu, W., Luo, Z., Wang, Y., Rham, N.T., Tuck, L., Pérez-Ri, I., Liu, L., Shen, Y., French, C., Auer, M., et al. (2018). Rapid pathway prototyping and engineering using in vitro and in vivo synthetic genome SCRaMbLE-in methods. Nat Commun 9, 1936.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Luo, Z., Wang, L., Wang, Y., Zhang, W., Guo, Y., Shen, Y., Jiang, L., Wu, Q., Zhang, C., Cai, Y., et al. (2018). Identifying and characterizing SCRaMbLEd synthetic yeast using ReSCuES. Nat Commun 9, 1930.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Luo, Z., Yang, Q., Geng, B., Jiang, S., Yang, S., Li, X., Cai, Y., and Dai, J. (2018). Whole genome engineering by synthesis. Sci China Life Sci 61, 1515–1527.

    Article  PubMed  Google Scholar 

  • Shen, M.J., Wu, Y., Yang, K., Li, Y., Xu, H., Zhang, H., Li, B.Z., Li, X., Xiao, W.H., Zhou, X., et al. (2018). Heterozygous diploid and interspecies SCRaMbLEing. Nat Commun 9, 1934.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ma, L., Li, Y., Chen, X., Ding, M., Wu, Y., and Yuan, Y.J. (2019). SCRaMbLE generates evolved yeasts with increased alkali tolerance. Microb Cell Fact 18, 52.

    Article  PubMed  PubMed Central  Google Scholar 

  • Mercy, G., Mozziconacci, J., Scolari, V.F., Yang, K., Zhao, G., Thierry, A., Luo, Y., Mitchell, L.A., Shen, M., Shen, Y., et al. (2017). 3D organization of synthetic and scrambled chromosomes. Science 355, eaaf4597.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mitchell, L.A., Wang, A., Stracquadanio, G., Kuang, Z., Wang, X., Yang, K., Richardson, S., Martin, J.A., Zhao, Y., Walker, R., et al. (2017). Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond. Science 355, eaaf4831.

    Article  CAS  PubMed  Google Scholar 

  • Ostrov, N., Landon, M., Guell, M., Kuznetsov, G., Teramoto, J., Cervantes, N., Zhou, M., Singh, K., Napolitano, M.G., Moosburner, M., et al. (2016). Design, synthesis, and testing toward a 57-codon genome. Science 353, 819–822.

    Article  CAS  PubMed  Google Scholar 

  • Richardson, S.M., Mitchell, L.A., Stracquadanio, G., Yang, K., Dymond, J. S., DiCarlo, J.E., Lee, D., Huang, C.L.V., Chandrasegaran, S., Cai, Y., et al. (2017). Design of a synthetic yeast genome. Science 355, 1040–1044.

    Article  CAS  PubMed  Google Scholar 

  • Shen, Y., Stracquadanio, G., Wang, Y., Yang, K., Mitchell, L.A., Xue, Y., Cai, Y., Chen, T., Dymond, J.S., Kang, K., et al. (2016). SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes. Genome Res 26, 36–49.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shen, Y., Wang, Y., Chen, T., Gao, F., Gong, J., Abramczyk, D., Walker, R., Zhao, H., Chen, S., Liu, W., et al. (2017). Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome. Science 355, eaaf4791.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Venetz, J.E., Del Medico, L., Wölfle, A., Schächle, R., Bucher, Y., Appert, D., Tschan, F., Flores-Tinoco, C.E., van Kooten, M., Guennoun, R., et al. (2019). Chemical synthesis rewriting of a bacterial genome to achieve design flexibility and biological functionality. Rroc Natl Acad Sci USA 116, 8070–8079.

    Article  CAS  Google Scholar 

  • Wang, J., Xie, Z.X., Ma, Y., Chen, X.R., Huang, Y.Q., He, B., Bin Jia, B., Li, B.Z., and Yuan, Y.J. (2018). Ring synthetic chromosome V SCRaMbLE. Nat Commun 9, 3783.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang, K., Fredens, J., Brunner, S.F., Kim, S.H., Chia, T., and Chin, J.W. (2016). Defining synonymous codon compression schemes by genome recoding. Nature 539, 59–64.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu, Y., Li, B.Z., Zhao, M., Mitchell, L.A., Xie, Z.X., Lin, Q.H., Wang, X., Xiao, W.H., Wang, Y., Zhou, X., et al. (2017). Bug mapping and fitness testing of chemically synthesized chromosome X. Science 355, eaaf4706.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu, Y., Zhu, R.Y., Mitchell, L.A., Ma, L., Liu, R., Zhao, M., Jia, B., Xu, H., Li, Y.X., Yang, Z.M., et al. (2018). In vitro DNA SCRaMbLE. Nat Commun 9, 1935.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xie, Z.X., Li, B.Z., Mitchell, L.A., Wu, Y., Qi, X., Jin, Z., Jia, B., Wang, X., Zeng, B.X., Liu, H.M., et al. (2017). “Perfect” designer chromosome V and behavior of a ring derivative. Science 355, eaaf4704.

    Article  CAS  PubMed  Google Scholar 

  • Zhang, F., and Voytas, D.F. (2018). Synthetic genomes engineered by SCRaMbLEing. Sci China Life Sci 61, 975–977.

    Article  PubMed  Google Scholar 

  • Zhang, W., Zhao, G., Luo, Z., Lin, Y., Wang, L., Guo, Y., Wang, A., Jiang, S., Jiang, Q., Gong, J., et al. (2017). Engineering the ribosomal DNA in a megabase synthetic chromosome. Science 355, eaaf3981.

    Article  CAS  PubMed  Google Scholar 

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Correspondence to Yingjin Yuan.

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Jia, B., Song, H., Liu, C. et al. Synthetic genome with recoding. Sci. China Life Sci. 62, 1096–1097 (2019). https://doi.org/10.1007/s11427-019-9595-8

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